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Case Studies of Seven Gene Families with Unusual High Retention Rate Since the Vertebrate and Teleost Whole-Genome Duplications

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Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts

Abstract

In the course of their evolution, the genomes of vertebrates have been subject to several events of whole-genome duplication (WGD): two rounds at the base of the vertebrates, a third at the base of the teleostean fish, and a few others in specific lineages like the salmonid fish or the Xenopus frogs among amphibians. Among the genes that were kept as duplicates long after the rediploidization process occurred, those that are involved in development, cell, and tissue diversification have the highest retention rates. In these categories fall gene families of different sizes that we previously investigated, namely genes that are implicated in the extracellular matrix formation that are the lectican, hapln, and adamts, or inducing a transcription or a cellular cascades: the transcription factors sox gene family, the nuclear receptors, the melanocortin receptors, cytoplasmic tyrosine kinases, and receptor tyrosine kinases. Here, we present an update of the expansion of these gene families due to the major vertebrate WGDs operated. Since the first occurrence of these WGDs, only six events of single gene duplication are reported, one being teleost fish specific and the second being sry in therians. This contrasts with the 71 ancestral genes that expanded in the jawed vertebrates to a total of 192 extant genes, and 75 additional genes in the teleost fish. We also discuss the ambiguities observed with the usual procedures of calculating gene retention rates. Interestingly, we observe that some of the gene families expanded in an intriguing regular manner. Those are also the ones that show very restricted lineage-specific losses. This feature is compatible and thus supportive of the autosomal-dominant deleterious mutation hypothesis that hampers the loss of the duplicated genes and explains their retention. Overall, the WGDs are shown to have amply participated in expansion of the gene families studied here, hence providing new potential for gene diversification, and by extension to the enhancement of molecular and cellular components of vertebrates.

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Abbreviations

WGD:

Whole-genome duplication

MYA:

Million years ago

MYR:

Million years

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Authors and Affiliations

  1. Univ Lyon, Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allée d’Italie, 69364, Lyon, France

    Frédéric G. Brunet, Thibault Lorin, Laure Bernard, Zofia Haftek-Terreau, Delphine Galiana & Jean-Nicolas Volff

  2. Physiologische Chemie, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany

    Manfred Schartl

  3. Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany

    Manfred Schartl

  4. Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA

    Manfred Schartl

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  1. Frédéric G. Brunet
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  1. Laboratoire Evolution Biologique et Modélisation, CNRS, Université d’Aix-Marseille, Marseille, France

    Pierre Pontarotti

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Brunet, F.G. et al. (2017). Case Studies of Seven Gene Families with Unusual High Retention Rate Since the Vertebrate and Teleost Whole-Genome Duplications. In: Pontarotti, P. (eds) Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Springer, Cham. https://doi.org/10.1007/978-3-319-61569-1_19

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